The combination of rapid technological advances and the development of new experimental model systems has propelled the area of beneficial microbes forward. Research over the last several years has provided overwhelming evidence that the health of humans, and likely most other animals, is dependent upon their associations with persistent, coevolved communities of microorganisms. Not only do these consortia of beneficial microbes play a critical role in day-to-day physiological homeostasis, but also they partner with the host's immune system to successfully resist pathogenesis. This latter role has taken on an increasing significance in an age of emerging infectious diseases and immunocompromised patients. The unprecedented advances in DNA sequencing technologies and associated bioinformatics analyses are now allowing researchers to transition from studying the composition of microbial communities to elucidating their metabolic potential even in complex host- associated microbial communities. The advances of omics approaches, i.e. transcriptomics, proteomics and metabolomics, are now helping to reveal the basis of host-microbe interactions at a functional level. The successful application of these approaches should elucidate the function of the microbiome and provide mechanistic insights into the interaction of microbial communities. The ASM Beneficial Microbes conferences are internationally attended meetings that bring together biologists in areas ranging from molecular genetics to metagenomics to systems biology and ecology to discuss the development of this frontier field of research. Based on the recent advances in the field, we obtained sponsorship from American Society for Microbiology (ASM) to organize a new Beneficial Microbe conference Functional and Mechanistic Insights into Host-Microbe Interactions. We are requesting funding for the support of United States and international scientists attending the upcoming meeting to be held in San Antonio, Texas, October 22-26, 2012. The meeting has six sessions devoted to exploring the current state of the field and defining new directions of inquiry. (i) Functional Analysis of the Human Microbiome will highlight new functional insights gained by transcriptomics, proteomics and metabolomics studies. (ii) Role of Beneficial Microbes in Health and Disease will have talks presenting results from animal models and clinical studies. (iii) Inter-kingdom Signaling will feature presentations from model systems that revealed broadly applicable molecular signaling. (iv) Beneficial Microbe-Immune System Interactions will feature research describing how beneficial microbes interact with the host immune system. (v) Role of Beneficial Microbes in the Environment will feature speakers that have pioneered approaches in environmental systems that are of direct relevance to medically important systems. (vi) Systems Biology of Symbiotic Systems will present whole systems approaches and analyses. PUBLIC HEALTH RELEVANCE: The role of beneficial microbes in health of humans is a new research area that represents a dramatic shift in the perception of microbes in general. The NIH funded human microbiome project has revealed the diversity of microorganisms that live in close association in and on the human body. They contribute to the health not only by preventing pathogenic bacteria from colonizing but by providing essential nutrients, stimulating the immune system and influencing the development. The goal of the 2012 meeting will be to emphasis on how metagenomics, metabolomics, and computational biology and modeling can be used to better understand host-microbe interactions. Understanding the role of microbes in health is critical to understand how disturbing the microbiome can lead to disease.